- Mar 2019
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these results by no means imply that early-life events do not affect microbiota assembly during infancy, nor do they question previous associations with disease or allergy (36, 37); our analyses only indicated that such events were not significantly associated with microbiome composition at adult age in the FGFP cohort
The authors acknowledge that these early-life events may affect microbiota development during infancy, but did not observe an effect of these events on the microbiota composition at adult age in their cohort.
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The cluster was predominantly composed of women, individuals with a lower weight, and participants with a longer transit time, as reflected both by stool consistency and time since previous relief. Both microbiota richness and evenness were elevated in this cluster.
When clustering the data based on taxonomic characteristics, one subset was predominantly female, having lower weight and low Bristol stool scale score and a longer time since last defecation. These individuals showed more equal and higher quantities of different microbial taxa.
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The presence of Fusobacterium could not be linked to any of the nonredundant covariates identified in this study, which could indicate the specificity of its association with colorectal cancer
The authors could not find any correlation between the presence of Fusobacterium and the set of 18 nonredundant covariates, suggesting that its presence is specifically associated with colorectal cancer.
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To achieve a balance between number of phenotypes of interest and rates of false discovery, a stepwise approach was applied.
The researchers wanted to ensure that the phenotypes of interest were not falsely correlated with microbiota genera. To avoid overfitting, they reduced the phenotypic data in different stages. By approaching the problem in a series of distinct stages, the researchers could determine the most important variables that affect the abundance and diversity of gut microbiota.
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Independently of gender, genus richness correlated positively with age, whereas total core abundance decreased
Researchers found that as both males and females age, the number of genera increases. However, age was negatively correlated with abundance of core genera.
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- Feb 2019
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science-sciencemag-org.ezproxy.neu.edu science-sciencemag-org.ezproxy.neu.edu
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autonomous vehicles (AVs) such as Google’s self-driving car covered thousands of miles
In October 2010, Google announced that its self-driving vehicles had collectively driven more than 200,000 kilometers (about 124,000 miles) on actual roads in California.
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This is a huge gap from a statistical perspective, but it must be understood as reflecting the state of public sentiment at the very beginning of a new public issue and is thus not guaranteed to persist
The authors note that there is a large gap in their confidence interval, which indicates that there is not public consensus. They point out that this is because autonomous vehicles are a relatively new issue, so different people have thought about it more or less.
As people get used to the idea and think about it more, the gap is expected to narrow.
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global outcome
Outcome on the whole community, not just individuals.
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without actually wanting to buy one for themselves
Again, the researchers found that participants thought self-sacrificing AVs are good for other people but would not want to buy one for themselves.
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broad public exposure and a disproportionate weight in individual and public decisions about AVs
Even though the situations where AVs would sacrifice their passengers are rare, these are emotional events that would have a large influence on the public despite their infrequency.
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autonomous driving in realistic urban environments
In 2007, the Defense Advanced Research Projects Agency (DARPA) hosted the DARPA Urban Challenge, which called for self-driving vehicles that could navigate a realistic city environment, and obey traffic rules while doing so.
The requirements for the challenge included passing slowly moving cars, merging into fast traffic, and parking in a parking lot.
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tickling-evoked vocalizations
Researchers have developed a new set of software that decodes ultrasonic rat vocalizations, including those that come from tickling!
Check it out with this video from Verge Science.
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dev-scienceintheclassroom.pantheonsite.io dev-scienceintheclassroom.pantheonsite.io
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O2
AAAS Annual meeting
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From our annotated research papers to our trainings and workshops, we're dedicated to bridging the communication gap between scientists and everyone else.
Beth, Shelby, and I will be in the AAAS Lounge starting at 10am on Friday.
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Improve science literacy with Science in the Classroom!
If you are interested in science communication, annotation, or just passionate about connecting students to #ActualLivingScientists, come see us!
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Science in the Classroom
SitC
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- Jan 2019
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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If the NPF-NPFR system were to function generally to signal the state of the Drosophila reward system, NPF levels should be increased by rewarding experiences other than mating, such as exposure to intoxicating levels of ethanol. To test this hypothesis, we exposed virgin males to ethanol vapor using an exposure paradigm previously shown to be rewarding (three 10-min exposures spaced by 1 hour) (4).
Throughout this paper, the researchers have been making the claim that activity of the NPF system signals the fly's "reward state." According to this theory, when the fly experiences something rewarding (such as mating), the amount of NPF in the brain and the activity of associated neurons increases, which in turn leads to a reduced urge to seek additional rewards (such as alcohol). To this end, they have shown that there is an increased amount of NPF in the flies' brains following mating. However, if their theory were true, then the opposite should also be observed. That is, the consumption of alcohol should also increase NPF levels in the brain, since alcohol is also a source of reward (just like mating).
To test this hypothesis, the researchers decided to measure NPF levels after exposure to both air and an alcohol vapor (the former being neutral/not rewarding, and the latter being rewarding). If their theory about NPF generally signalling reward were true, one would expect to see increased levels of NPF in the brain following exposure to alcohol (just like was observed following mating in Figure 2A).
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heads of males subjected to different sexual experiences: rejected-isolated, virgin-grouped, and mated-grouped
Since past work in Drosophila, mice, and C. elegans has shown that altering NPF/NPY can affect how organisms react to alcohol, the researchers in this study hypothesized that sexual deprivation might lead to changes in levels of NPF in the flies' brains, which in turn caused them to consume more alcohol. To test this, they extracted the brains from male flies with three distinct sexual histories (mated, virgin, and sexually rejected), and measured their NPF levels.
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NPF–NPF receptor (NPFR)
All neuropeptides in the brain work by attaching to specific receptors found on the surface of cells. Think of the cell surface as a wall, the receptor as an electrical outlet, and the neuropeptide as a plug. In order for the neuropeptide (plug) to have any effect, it has to successfully attach to the correct receptor (socket). Furthermore, a particular neuropeptide (say, a three-pronged plug) cannot attach to just any receptor (for example, a two-pronged socket). The receptor and the neuropeptide have to match in order for the system to have any effect.
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Finally, we sought to establish whether there was a role for the repellant chemosensory cue
Since cis-vaccenyl acetate (cVA) is used by females to turn away unwanted mating attempts by males, it is only released by females who have already mated. Virgin females, who may still be looking to mate, do not release this chemical cue. This difference raises the possibility that the increased preference for alcohol amongst the rejected males could be because they smelled this chemical cue (which the mated male flies would not have smelled).
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males were exposed individually to decapitated virgin females on the same schedule as the rejected-isolated cohort, using a protocol that results in courtship suppression
To test this possibility, they exposed the virgin male flies to dead female flies. These virgin males were still exposed to the visual cue of a female fly (especially the rear half of the body where mating occurs). However, they were neither able to mate, nor were they exposed to active rejection by a female.
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we compared males that differed in sexual experience but not in housing conditions—that is, mated and virgin males that were both group-housed.
For the first follow-up experiment, the researchers ensured that both the mated male flies and the virgin male flies were housed in large groups (consisting exclusively of other male flies). This was done to see if social isolation (as the virgin male flies in the initial experiment might have experienced) might have been the cause for the alcohol preference.
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was consistently higher for the rejected-isolated cohort
The researchers found that when given a choice between normal food and alcohol-mixed food, male flies who had mated with female flies did not prefer the alcohol, whereas male flies who had been rejected by the female flies did prefer the alcohol.
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We used two distinct sexual experiences to generate two cohorts of male flies.
To test the effect of sexual experience on alcohol consumption, the researchers first had to create two groups of male flies, each with a different sexual history. They did this by allowing one group to mate freely with multiple different females for four days. This became the "mated-grouped cohort." The second group was only exposed to female flies who had already mated. Female flies who have already mated once will not mate a second time until they have laid their eggs. For this reason, the second group of males experienced repeated sexual rejection by the mated females for four days. This became the "rejected-isolated cohort." These two cohorts, (one mated and the other sexually rejected) could then be tested for the differences between them.
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quantify depletion
The authors used "depletion scores" to compare nucleases. A depletion score quantifies how much expression was reduced by a specific nuclease. The higher the score, the more expression was "depleted."
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expression vector
A type of vector that can use the cell's protein synthesis machinery to express the genes that it carries.
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mutagenesis
Creating genetic mutations.
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assayed
Testing a material to figure out its composition and quality.
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we compiled evidence for the earliest dog remains across Eurasia
Remains aren't the only type of archaeologically significant findings. Recently, cliff drawings were found in northwest Saudi Arabia depicting hunting dogs wearing leashes. These carvings date back to more than 8000 years ago, making them the earliest depictions of dogs ever found.
Read more in Science Magazine: https://www.sciencemag.org/news/2017/11/these-may-be-world-s-first-images-dogs-and-they-re-wearing-leashes
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assigned to one of four major well-supported haplogroups (groups A to D)
Scientists studied the mitochondrial DNA of 654 domestic dogs and 38 wolves, and were able to separate the dogs into four main clades (A, B, C, D), groups that contain an ancestor and all of its descendants. A fifth clade, E, was a very small, isolated group.
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We used principal components analysis (PCA), D statistics, and the program TreeMix (12) to further test this pattern.
Three tools for mining the data for ancestry information.
Principal components analysis (PCA) simplifies the data. The number of variables is reduced but the trends and patterns are retained.
D-statistics detects admixture events; it is used to detect gene flow between closely-related species.
TreeMix is a genetics computer program used to estimate ancestral relationships. It can detect population splits and migration events.
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Paleolithic
Refers to the earliest stage of the time period known as the Stone Age. The Paleolithic period ran from approximately 2.6 million years ago all the way up to about 10,000 B.C.E.
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occurred in Europe (7), Central Asia (8), or East Asia (9)
Wang et al. studied the genomes of 12 gray wolves, 27 ancient dog breeds, and 19 diverse dog breeds from all over the world. They discovered that dogs from Southeast Asia have higher genetic diversity and their DNA is less mixed, meaning that they are the most related to wolves; they estimate that domestication occurred there 33,000 years ago. Dogs were isolated to this region for several thousand years, and about 15,000 years ago they migrated to other parts of the world.
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- Dec 2018
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Ellstrand and Schierenbeck 2000
In 2000, Ellstrand and Schierenbeck proposed hybridization as a catalyst for the evolution of invasion.
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Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.
This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.
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Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.
This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.
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Populations of white-sand and terra firme ecotypes of Protium subserratum were attacked by herbivore assemblages differing in both abundance and species composition, exhibited significant differences in growth and defense allocation, and expressed qualitatively different secondary compounds. That these phenotypic differences occur in populations involved in incipient (or recent) speciation is consistent with the hypothesis that herbivores interact with environmental gradients to promote the evolution of habitat specialization in plants
The ultimate summary of the whole paper. It explains why there needed to be side experiment analyzing different variables that would then clarify the conclusion that supports the given hypothesis.
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we believe that the differences in defense strategy we find agree with a growing consensus that plant defense traits are involved in diversification
In this study from 2009, the results of diversification, when subpopulations with independent genetic modifications emerge, were concluded not to be homogenous in their relation to performance. This concept is further analyzed through this experiment in the speciation and the variation of defense strategies.
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The existence of this trade-off has been well supported by many different temperate and tropical studies looking at allocation to growth and defense in plants adapted to different light and nutrient availabilities, both within species
The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.
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Finally, it is important to recognize that our sampling was limited to juvenile plants and lasted only 12 months. Insect herbivore populations can strongly vary in different years, and thus, it is possible that our sampling missed important herbivores that are associated with P. subserratum.
This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.
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We found that insect herbivores collected from Protium subserratum showed strong patterns of dissimilarity across different habitat types (Fig. 3). Moreover, we found significantly more insects feeding on terra firme plants than on white-sand plants, correlating with the large differences in resource availability between the habitat types. Taken together, these results suggest that there exists substantial variation in diversity and abundance of insect herbivores associated with P. subserratumacross white-sand and terra firme habitats.
The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.
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unlike most members of the family Burseraceae, P. subserratum does not yield measureable amounts of monoterpenes and only trace amounts of sesquiterpenes
Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.
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Terra firme populations exhibited significantly greater height and leaf growth and allocated more to chlorophyll production than white-sand populations in both soil types, demonstrating that different growth strategies have a genetic basis
The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.
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Differences between sites, habitat types, and their interaction explained 14%, 15%, and 11%, respectively, of the variation in herbivore species composition among the four sampling locations
This is explaining how the variation of herbivore species is closely related to the variation of plants in the location. The study explains how certain insects prefer to ingest other substances that can be identified, allowing the experimenter to see how the insects lived in accordance to where the plants where, instead of plants appearing around certain species of insects.
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differences among the dominant herbivores, the species composition of the entire P. subserratum herbivore fauna exhibited high turnover among sites and habitats
The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.
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We compared absolute and qualitative differences in leaf defense. First, we compared the dry mass of leaf defense chemicals in a linear model with soil type and study region as independent variables. Second, we tested whether habitat type, sampling site, or the interaction of the two, was a significant determinant of the relative allocation among flavan, flavone, quinic acid derivatives, and oxidized terpenes in each plant using a factorial analysis of variance.
When doing comparison, it helps to create a table to have a better understanding on the differences in leaf defense.
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Second, we used a factorial analysis of variance (McArdle and Anderson 2001) to assess whether habitat type, sampling site, or the interaction of the two was a significant determinant of herbivore species composition.
This was done to determine the different variables that affect insect populations and which ones were more important than others. With this information they set the parameters to create an observable experiment with a limited amount of discrepancies.
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In order to study the evolutionary processes involved in habitat specialization and the role of insect herbivores, an ideal study system would include recently derived sister species, or diverging lineages undergoing incipient speciation in different habitats.
Main goal for the paper.
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A long-standing hypothesis has linked escalation in plant defense that allows escape from insect herbivores to range expansion and speciation (Ehrlich and Raven 1964). Such escalation can include increases in the diversity of defense strategy (novel defense types), increases in the total amount of defense investment, or both (Agrawal et al. 2009). Range expansion, or merely an imperfect match between the distribution of plants and their natural enemies, may confront plants with different herbivore assemblages and/or variation in habitat resources across their range (Thompson 2005, Züst et al. 2012). This variation, in turn, may accelerate the evolution of differing defense strategies across habitats. Alternatively, natural enemies may not be major selective agents driving habitat specialization. In this case, we would predict that there would be few qualitative and quantitative defense differences between habitats, especially when diverging lineages of host plants occur in close proximity and also experience some gene flow across the habitat boundary.
The main point the author is trying to make here is that there is a direct correlation between increase in plant defense and increase in land covered by plants as well as speciation of plants. He also explains that due to the expansion, rapid evolution of defenses begin to take place. The herbivores eating these plants do differ in tactics from region to region, increasing the amount of different defense strategies in the plants. He explains an alternative viewpoint stating that predators do not influence speciation much, therefore defenses are similar amongst most plants.
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promote very different defense allocation strategies for different plant species depending on the type of defense employed (i.e., their elemental constituents and biosynthetic pathways), as well as the nature of resource limitation across habitats (i.e., light, nutrients, or water) (Bryant et al. 1983, Herms and Mattson 1992).
This statement addresses the variables that must be acknowledged when trying to analyze different plants and their different defense strategies. The "resource limitation across habitats" that the author is referring to is what in the environment can the plant use to defend itself in its habitat from threats such as herbivorous insects.
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the optimal defense allocation may be affected by differential costs of tissue replacement across habitats
Herbivorous insects are constantly eating plants, creating competition between the plants and insects. What is stated here is that optimal defense may be impacted by the plants environment, giving it access to certain nutrients and materials needed to produce the desired defense mechanism, such as poisonous leaves or indigestible tissues.
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the species composition and relative abundance of herbivore communities may turn over among habitats because herbivores are affected by habitat quality, structure, and interactions with predators
The idea in place here is the observation of evolution in herbivorous in correlation to the environment and all its factors.
The study provides proof of evolution in herbivorous in respect to the environment by analyzing adaptive radiation. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous.
To further understand adaptive radiation watch [(https://www.brightstorm.com/science/biology/evolution/adaptive-raditaion/)
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But little is known about the mechanisms underlying the evolution of habitat specialization and the extent to which herbivores contribute to phenotypic divergence during the speciation process,
The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.
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Herbivores play an important role in habitat specialization because they can magnify the differences in resource availability across habitats
The sources mention, that in a habitat with a low amount of productivity there is a good amount of strong plants/ plants that are "rich in chemical defenses". In a habitat with lower productivity, the plants are thought to do this in order to increase its life span. Therefore, as the productivity and the amount of herbivores changes the strength and and amount of the resources changes.
For more information check out: Tropical Blackwater Rivers, Animals, and Mast Fruiting by the Dipterocarpaceae
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Assemblages of insect herbivores were dissimilar between populations of ecotypes from different habitats, as well as from the same habitat 100 km distant.
In Africa, there is a food crisis leaving millions of people without corn, a very important crop for Africa. The reason for these crops not being edible is that a certain species of worm invaded a field of corn and rapidly spread to neighboring farms, killing millions of corn crops leaving thousands hungry. This proves the point how insects differ from each-other depending on what type of plants are around, since this worm is always flocking to this one crop.
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reciprocal transplant experiment
The reciprocal transplant experiment is an experiment where organisms from two or more environments are introduced to each other.
The experiment is commonly used to test how well the organisms adapt, and sources of growth variation (genetic or environmental).
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morphological
Relating to the form or structure of things, having to do with somethings physical appearance/structure.
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qualitative
Referring to something's qualities, not numerical but categorical. Can be described with words, not numbers.
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chromatography
A process of separation where components are distributed; in this case the chemical components of the gas.
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pubescence
Pubescence in this context means small hairs or short down on the leaves and stems of various plants.
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phenotypic plasticity
A genotypes ability to change as an adaptation to the environment. This refers to the plant's distribution of resources.
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regression
Regression analysis is a statistical model made up up of a series of processes used to understand how the dependent variable changes when any of the independent variables are modified.
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Protium subserratum Engl.
The Protium subserratum Engl. is the name of a species that has distinct defense mechanisms and is in the genus Protium, which are flowering plants in the family Burseraceae.
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parapatric distribution
Parapatric distribution refers to a distributional pattern where pairs of taxa are partially overlapping or have separate but adjacent distributions, typically along common boundaries.
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incipient speciation
incipient meaning the beginning of a process and speciation is the diverging of similar species into two or more differing species due to evolution
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reciprocal
Having to do something to both side, the bearing or binding of 2 parties equally.
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gradients
Describes different sides in comparison to each-other, a gradient can be in reference to water pressure as well as many other things.
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herbivore to circumvent or detoxify defenses
An example of this defense is how a monarch butterfly caterpillar holds on to a milkweed's toxins to then use it for their own protection and survival.
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beta-diversity
The over all number of differing variations in the region.
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Environmental gradients
A progressive change over time of the nonliving factors that make up an environment examples of nonliving factors in an environment would be altitude, temperature, depth, humidity etc.
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habitat-mediated speciation
Habitat-mediated speciation is the emergence of different species throughout evolution, brought about by the natural environment and its effects.
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chlorophyll
Chlorophyll is a green pigment that is found in the chloroplasts of algae and plant cells. It works well to absorb sunlight which is then used to make carbohydrates, through a process called photosynthesis.
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hemipterans
Hemipterans are an order of insects that share the common characteristic of a sucking mouthpart. Beatles are different because they have chewing mouthparts.
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chrysomelid beetles
Chrysomelid beetles are commonly known as leaf bugs. Their food course are leaves .
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ecotypes
The word ecotypes refers to different species of a plant or animal living in a specific habitat.
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plant defense allocation
Allocation refers to the distribution of something for a specific purpose.
Plant defense allocation is one of the ways a plant can protect itself, its resources and reduce the impact of herbivores.
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posits
Posits are statements or arguments that are assumed to be true.
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Herbivores
Herbivores are animals who get their energy by eating plants.
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flora
Flora refers to the diverse plant life that is within a specific region, or time period.
In this case, it's the plant life in the tropics; tropical flora.
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phyletic
Has evolved in some way.
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invasive species
any kind of living organism that is not native to an ecosystem and causes harm. They can harm the environment, the economy, or even human health.
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parasites
An organism that benefits from living from a host which is another organism.
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paraphyletic
having a common ancestor.
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blastula
early stage of development
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asexually
Reproduction without a male and female.
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glycoproteins
proteins that have carbohydrate groups.
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heterotrophic
An organism that can make food.
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transcriptomes
All the genes expressed by mRNA
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conservation
means preserved.
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sequencing
In this case, RNA and DNA are aligned to facilitate gene expression.
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genomes
a complete set of genes that carry information in an organism.
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invertebrates
an animal that does not have a backbone
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metazoan
means a living organism that is multicellular.
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a prominent position in current scenarios
Looking at phenology through generations can aid us in understanding how the globe is changing. The video linked below shows how recording events can help humans connect and interact with biotic communities. URL: http://climatewisconsin.org/story/phenology
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Ants are important predators in tropical forest ecosystems
The authors cited performed studies that ants are a very important predators in tropical forest ecosystems.
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Treatments applied to caterpillars were: (1) no barriers (no tanglefoot/no cage), (2) tanglefoot present/no cage, (3) no tanglefoot/cage with holes present, (4) tanglefoot present/cage with holes present, (5) no tanglefoot/cage present, and (6) tanglefoot present/cage present.
These are the parameters made to make sure that the experiment itself is not biased and there are different variables being tested.
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Field observations revealed that sheer caterpillar size was a fair defense against these ants;
Authors found out in the field that the sheer caterpillar size was a mechanism of defense to against predators.
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osmeteria
A defensive organ found in all papilionid (from the family of Swallowtail butterflies) larvae, in all stages.
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pupate
To become a pupa.
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Pseudomyrmex gracilis received the highest final score at 52, and C. floridanus had the next highest score at 40; both C. ashmeadiand C. planatus received lower scores of 24
Based on species abundance, the Pseudomyremx gracilis received the highest score.
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overdispersion
The presence of greater variability (statistical dispersion) in a data set than would be expected based on a given statistical model.
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logistical constraints
The planning, implementation, and coordination of the details of a business or other operation.
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Gentry plots consistently emerge as the best compromise
Overall, 0.5 hectare gentry plots were the best method.
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Fig. 1.
Figure 1 shows how the coefficient of variability changed for the different types of plots used. The use of smaller plots had a smaller CV meaning that the results had low variance and did not stray much from the standard deviation compared to the larger plots.
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The 1 ha plots, despite their relatively high cost to implement (Table 1), were more efficient to inventory than the smallest plots, although 1 ha plots were still inferior to the 0.5 ha modified Gentry plots.
It was found that the plots that were smaller than 1 hectare had better results than the plots that were larger (1 hectare).
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Markov Chain Monte Carlo methods
MCMC methods are a class of algorithms for sampling from a probability distribution. By constructing a Markov chain, a sample of the desired distribution by observing the chain after a number of steps.
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thaw degree days (TDDs)
TDDs are negative when over zero degrees celcius (thawing) and positive when under zero degrees celcius (freezing). Best for comparing arctic temperatures across specific time periods.
http://psc.apl.washington.edu/nonwp_projects/landfast_ice/freezing.php
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graminoid
Herbaceous (having no stem above ground) plant with grass-like features.
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Remote sensing
It may take a lot of work to study plants at extreme environments like the tundra. Remote sensing facilitates the studying of plants without having to come in contact with them.
Watch this video by MonkeySee https://www.youtube.com/watch?v=sBI3MIbzIBA
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Oberbauer
National Science Foundation – Ecosystems. Causes and implications of dry season control of tropical wet forest tree growth at very high water levels: direct vs. indirect limitations (CARBONO - VERANO project).
National Science Foundation – Polar Programs. Arctic Observing Networks: Collaborative Research: Sustaining and amplifying the ITEX AON through automation and increased interdisciplinarity of observations (AON)
NSF-Arctic Natural Sciences. Collaborative Research; cold-season gas exchange of arctic plants - resolving winter carbon and water balances of Alaskan arctic tundra (Coldseason project).
NSF -IPY Arctic Observing Networks Study of Arctic ecosystem changes in the IPY using the International Tundra Experiment. (ITEX-IPY)
DOE-NICCR. Response of carbon dioxide, water, and energy exchange of peat and marl wetlands in the Florida Everglades to changes in hydroperiod (Evergladesflux).
NSF-Biocomplexity. Biocomplexity Associated with the Response of Tundra Carbon Balance to Warming and Drying Across Multiple Scales. Barrowbiocomplexity (this project has sunsetted). Effects of increased season length on plant phenology, community composition, productivity, and ecosystem carbon fluxes in Alaskan tundra Season project (this project has sunsetted)
Carbon stockes and fluxes in a tropical rain forest in Costa Rica Carbono project
NSF- Integrated carbon program. Understanding interannual NEE variability in a tropical rain forest using constrained estimates of carbon exchange. S.F. Oberbauer, D.A. Clark, M. Ryan, D.B. Clark. Carbono-Towers
National Science Foundation - Biocomplexity of the Environment Coupled Biogeochemical Cycles. Complex interactions among water, nutrients and carbon stocks and fluxes across a natural fertility gradient in tropical rain forest. (CICLOS PROJECT).
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spatial abundance pattern.
Spatial and temporal abundance patterns relate to the study. Temporal abundance pattern has to do with quantity over a period of time and spatial abundance patterns have to do with quantity over a particular area of space.
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temporal monitoring studies
Temporal monitoring is monitoring that is conducted over time.
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focal species
Focal species are species that are extremely sensitive to the changes in an environment.
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However, can marine reserves also benefit large, roving reef predators that are potentially mobile throughout their life?
This question sheds light on a topic regarding the suitability of marine reserves not only as a permanent safety harbor for recovery and expansion of the species but also the temporary inhibition of the space by species that are mobile, whether they would use the space to breed for protection or for a stable source of food and shelter.
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Marine reserves can clearly enhance exploited coral reef species that have relatively sedentary adult life-stages, in which some individuals live almost exclusively within reserve boundaries
A study in 2 June 2009 conducted by Philip P. Molloy explored the relations with the age of the marine reserves and of the recovery of different species of fish. The studies showed that older marine reserves (15 years and older) were more effective than younger ones. They harbored more fish.
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site-fidelity
Side-fidelity, also known as philanthropy, is the likelihood of a particular organism to stay in a set habitat, or to return to it. There are many reasons to this, such as breeding and food abundance.
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Florida Red Tides
Discolored red patches of coastal waters caused by harmful algal bloom.
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phenology
the study of cyclic and seasonal natural phenomena, especially in relation to climate and plant and animal life.
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larger fish have greater thermal inertia and increased cardiac capacity
Thermal inertia is the ability of a body or object to maintain its temperature when ambient temperature changes. Larger objects have higher thermal inertia, so larger fish lose heat more slowly than smaller fish. Larger fish also have larger hearts, which can pump more blood.
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metabolic scope
is a suitable gauge for assessing the environmental influence on fish biological performance (Fry 1971)
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The largest size-based differences in energy intake were also observed in October (Fig. 6 and table S3), indicating that thermal niche expansion in this endothermic species results in high energetic reward.
The increased temperature range allowed the tuna to forage and obtain energy more efficiently.
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ILD
Isothermal Layer Depth
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SST
Sea Surface Temperature
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spatiotemporal information
Information relative to the space and time of the tagged fish.
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Lower energy intake was observed during late summer (August and September), when bluefin tuna are moving up through the Southern California Bight (28° to 32°N).
Lower energy intake during migrations.
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heterogeneity
The quality or state of being diverse in character or content.
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interpolated
insert (something of a different nature) into something else
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Energy intake and thermal excess were positively correlated with body size as measured by the curved fork length (CFL) of tagged tunas
A big tuna (large body size) requires more energy which means it needs to feed from a higher amounts of prey or big preys. Consequently, the heat production is higher provoking a thermal excess.
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CCLME
California Current Large Marine Ecosystem (CCLME), along the Mexico and California coasts
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HIF
Stands for Heat Increment of Feeding.
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peritoneally
Located in the abdominal cavity.
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Here, we quantify energy intake in 144 wild Pacific bluefin tuna in the CCLME on over 39,000 days (fig. S1), using HIF measurements from implanted archival tags. We estimate energy intake using a model developed with laboratory data collected from similar-sized bluefin tuna (22) at a range of ambient temperatures.
By analyzing the temperatures of digestion in bluefin tuna, the author can draw conclusions as to what the tuna is eating, how much energy is gained from the meal, and how often the tuna eats. HIF means heat increment of feeding.
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hitherto
Until now or until the point in time under discussion
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viscerally
Internal organs within the main cavities of the body.
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sinuous
means having many curves or turns.
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a proxy for feeding
authorization of feeding.
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Pacific bluefin tuna (Thunnus orientalis)
The Pacific bluefin tuna are smaller than the Atlantic bluefin tuna. It reaches the maximum length of 3m and a maximum weight of 540kg.
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quantified
express or measure of quantity.
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garnered
means gathering or collecting.
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niche
conditions under which an animal lives
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commercial cultivation in artificial settings
Read More: In vitro seed germination and seedling growth of an endangered epiphytic orchid, Dendrobium officinale, endemic to China using mycorrhizal fungi (Tulasnella sp.)
Tan et al. 2014
http://www.sciencedirect.com/science/article/pii/S0304423813005578
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Fig. 2 Terrestrial C loss rates from stream reaches increased with N and P concentrations.
Graph illustrating the loss of terrestrial carbon.
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Fig. 1 Terrestrial C residence time was approximately halved with experimental nutrient enrichment. Increased nutrient inputs (+) reduced terrestrial particulate C residence time (–) and increased export of fine detrital particles (+) and respiration rates [which increased on C substrates (11) but decreased at reach scales; +/−]. Inset graph: Reach-scale leaf litter loss rates were faster in enriched (dashed lines) than in reference (solid lines) streams; the inverse of these rates is residence time. Colors correspond to the same years in (A) (reference versus enriched streams; N+P experiment; n = 12 annual rates) and to the same streams in (B) (pretreatment versus enriched years; N×P experiment; n = 15 annual rates). Data shown for litter loss are untransformed but were natural log–transformed for analyses and the calculation of loss rates (k, per day). The larger image depicts terrestrial organic C inputs, which enter as leaf litter, wood, and dissolved organic carbon (DOC), and outputs as hydrologic export (fine and coarse particles, DOC) and respired CO2 in deciduous forest streams, using an image of one of the N×P experimental stream sites.
Image illustrating the various sources of carbon observed in the experiment.
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Experimental nutrient additions accelerate terrestrial carbon loss from stream ecosystems
Effects of Nutrients on Stream Ecosystems
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Editor's Introduction
Within an ecosystem, there are external factors which may threaten the balance. Effects on stream ecosystems are heavily influenced by nutrients. Phosphorus, nitrogen, and carbon balance is essential to keep the ecosystem consistent. When carbon is released from the streams, it does not easily re-enter and goes into different forms. An excess of nutrients and the lack of standards for these ecosystems may be detrimental. Why is it important to conduct such research? Why is it important to care for and monitor other ecosystems?
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D. Anglesea, C. Veltkamp, G. H. Greenhalgh, The upper cortex of Parmelia saxatilis and other lichen thalli. Lichenologist 14, 29–38 (1982).
An important paper that shows the role of glue-like polysaccharides in filling the spaces between fungal cells and holding the lichen together. The yeasts described in this paper live in this filler zone.
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I. A. Aschenbrenner, T. Cernava, G. Berg, M. Grube, Understanding microbial multi-species symbioses. Front. Microbiol. 7, 180 (2016).
This paper highlights the possible role bacterial symbionts might play in lichen formation and maintenance.
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R. Honegger, Developmental biology of lichens. New Phytol. 125, 659–677 (1993).
This review discusses how lichens develop, their structure and function, their growth patterns, and how thalli are differentiated.
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the production of which often does not correlate with the lecanoromycete phylogeny
Researchers had previously noted the presence of secondary metabolites in the lichen cortex. The researchers initially looked for a correlation between the main fungal species (lecanoromycetes) and the production of these secondary metabolites, but could not determine a correlation.
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Most macrolichens possess a basic two-layer cortex scheme consisting of conglutinated internal hyphae and a thin, polysaccharide-rich peripheral layer
Perhaps this is easiest to understand with a picture. If you look closely, you can see two layers within the cortex.
Photo from University of California Berkeley's Museum of Paleontology.
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popular fungal barcode
AP Biology Standards EK1.A.4: Molecular, morphological, and genetic information of existing and extinct organisms add to our understanding evolution. Biochemical and genetic similarities, such as DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.
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teleomorphic
The sexual life stage of the fungi where cells become polarized, or have two obvious ends, and through cell division form long structures called hyphae. In some fungi, the individual cells are multinucleate. Only some fungi are capable of this form of reproduction; for example, baker’s yeasts used in beer fermentation are not able to grow this way.
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We therefore developed protocols for fluorescent in situ hybridization (FISH) targeting specific ascomycete and cystobasidiomycete rRNA sequences.
A molecular probe is created against a specific DNA sequence, in this case rRNA from either ascomycetes or basidiomycetes. The probe is designed with a recognizable tag on the end. Then a second probe is used to match the first probe, and finally a third probe to match the second one with a fluorescent tag on it. By using multiple probes we can amplify even the smallest signals to our first probe. These probes are then mixed with a biological sample that is fixed in place. If fluorescence is observed the probe has found a target.
In some experiments, as in this example, researchers use multiple probes in a single experiment. This provides information about how close two organisms of interest are in a given sample.
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incorporated into a broader sample of published cystobasidiomycete rDNA sequence data
Often researchers only publish a single gene for a newly described taxon, as it is sometimes too expensive to generate sequence information for the entire genome. When research first began working with DNA sequence data to determine evolutionary relationships it was decided that the ribosomal DNA (rDNA), shared by every living thing, was the best single gene to determine evolutionary relationships between taxa. Currently this is hotly debated, however, the use of rDNA is still very common in eukaryotic taxonomy.
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using gene sequences inferred from our transcriptome data set and other available genomes (table S1).
Phylogenies are often used to determine the taxonomy of a lineage, that is the evolutionary context of an organism within the greater tree of life. The researchers could recognize that the new symbiont was a basidiomycete from the sequence information, but only by comparing the sequence information of the new organism to the previously known organisms can we determine when and from which ancestor the new species evolved. To account for the millions of years that have passed after all the basidiomycetes diverged from one another, the researchers incorporate as much sequence data as possible. Here, they use 349 loci to determine the placement of the new lineage.
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radiations
Genetic or molecular diversification. As genetic changes occur over time (evolution), diversity will increase within a group, illustrated by branching on a phylogenetic tree.
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single nucleotide polymorphisms (SNPs)
A variation in a single base pair (A, T, C, G) in a DNA sequence. Some sites in a gene are more likely to mutate than others. Phylogenetic information is based on genetic differences between organisms, and single nucleotide polymorphisms (SNPs) provide the most information.
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transcriptomics
A way to study what genes are being expressed and at what level. All messenger RNA (mRNA) is collected from a sample and each mRNA is counted to measure gene expression. The more copies of mRNA associated with a specific gene, the more highly expressed that gene is.
To learn more about gene expression through transcription, see https://www.hhmi.org/biointeractive/dna-transcription-basic-detail
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amplicon sequencing
Refers to sequencing of target genes obtained by a procedure called polymerase chain reaction (PCR) using gene-specific primers. Amplicon sequencing provides a snapshot of the microbial populations in an environment.
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lichen thalli
Generally, lichen thallus (singular form of thalli) types fall into four basic growth forms: crustose, squamulose, foliose, and fruticose.
Lichen thalli can develop into a diverse range of structures: multiple-branched tufts; flat, leaf-like structures; filamentous structures; and aggregates of tiny plates.
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a symbiosis
Next Generation standard LS2.A: Interdependent Relationships in Ecosystems
AP Biology Standards EK2.D.1: All biological systems from cells and organisms to populations, communities, and ecosystems are affected by complex biotic and abiotic interactions involving exchange of matter and free energy.
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parasites
Organisms that live on or inside another organism and get their food from or at the expense of their host.
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nomenclatural synonyms
The naming of all living species is governed by rule books called codes of nomenclature. According to these rules, if it is discovered that the same organism has been named twice, for instance by different people who didn’t know each other at different times, then the older name is given priority and the second name becomes a “synonym."
In this case, studies of the main fungal partner in Bryoria fremontii and B. tortuosa showed that they are genetically identical, and thus the two names technically should become nomenclatural synonyms. If this rule would be followed through here, the older name (Bryoria fremontii) must be used because it is older. However, the authors chose not to follow the rule so that they would still have names to use to discuss the two different lichen phenotypes
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between a single fungus, usually an ascomycete, and a photosynthesizing partner
Several natural scientists in the mid-1800s began to suspect that the lichen was in fact a mixture of two organisms, but it was the Swiss botanist Simon Schwendener who demonstrated that lichens were composed of fungi and algae for the first time in 1869. Initially, he thought the relationship must be antagonistic—that the fungi were “imprisoning” the algae. Ten years later, the German botanist Anton de Bary proposed the idea of mutually beneficial symbiosis for the lichen system.
Read more about Schwendener's discovery and the controversy it caused here. Find the full PDF in the "Related content" tab.
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These data suggest that the gall-inducing form of Cyphobasidium completes its life cycle entirely within lichens.
AP Biology Standards EK4.B.2: Cooperative behavior within or between populations contributes to the survival of the populations, i.e. mutualistic relationships.
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phylogenomic tree
AP Biology Standards EK1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
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analysis placed the basidiomycete as sister to Cystobasidium minutum (class Cystobasidiomycetes, subphylum Pucciniomycotina) with high support
AP Biology Standards EK 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
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mRNA transcriptome sequencing
AP Biology Standards EK 1.B.1: DNA and RNA are carriers of genetic information through transcription, translation, and replication.
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genetically distinct strain of the basidiomycete
AP Biology Standards EK1.A.4: Biochemical and genetic similarities, such as DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.
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The assumption that stratified lichens are constructed by a single fungus with differentiated cell types is so central to the definition of the lichen symbiosis that it has been codified into lichen nomenclature
Check out this video from SciShow where Hank Green interviews lead author, Toby Spribille, about his research and conclusions. The interview describes the findings, clarifies the different groups of fungi discussed, and describes how they are related to one another. Spribille describes the differences between Ascomycetes and Basidiomycetes and the radiations in the fungal lineage.
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V. Ahmadjian, The Lichen Symbiosis (John Wiley & Sons, 1993).
This paper describes the cortex deficiencies of lichens grown from only the two previously known symbiotic partners.
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In B. fremontii, differential transcript and cell abundance data, along with physical adjacency to crystalline residues, implicate Cyphobasidium in the production of vulpinic acid, either directly or by inducing its synthesis by the lecanoromycete.
The data presented in this paper mean that it can’t be ruled out that the newly identified basidiomycete is involved in vulpinic acid formation. Questions to be tested in the future include whether basidiomycetes produce the acid directly, or whether their presence causes the other fungal players to produce the acid themselves.
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The discovery of ubiquitous yeasts embedded in the cortex raises the prospect that more than one fungus may be involved in its construction, and it could explain why lichens synthesized in vitro from axenically grown ascomycete and algal cultures develop only rudimentary cortex layers
These Cyphobasidium cells were found throughout the lichen, and show evidence of living their whole life cycle within the lichen. Therefore, at this point, it cannot be ruled out that these basidiomycetes might be integral to the structure, phenotype, and formation of some lichen species.
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Consistent with the transcript abundance data, these cells were more abundant in thalli of B. tortuosa (Fig. 3), where they were embedded in secondary metabolite residues (movie S1).
The results of imaging showed that more basidiomycete cells were present in the lichen that produce vulpinic acid (B. tortuosa). This result supported the gene expression analysis results.
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As a whole, these data indicate that basidiomycete fungi are ubiquitous and global associates of the world’s most speciose radiation (14) of macrolichens.
The researchers demonstrated, using rRNA analyses, that the new basidiomycete probably evolved with the lichen species. They showed that different lichens carried different basidiomycete strains. They concluded that basidiomycete symbionts are present in many lichens, and many lichen carry a specific strain.
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Restricting our analyses to Ascomycota and Viridiplantae revealed little differential transcript abundance associated with phenotype
The scientists found that genes in Ascomycota (the mycobiont in both lichens) and Viridiplantae (both lichen's photobiont) were expressed similarly in both lichens. Therefore, they concluded it was unlikely that a common gene was causing the production of vulpinic acid in one lichen but not the other. Therefore, the phenotypic differences between two lichen species could not be explained simply by looking at gene expression in the symbionts.
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attempts to culture the basidiomycete from fresh thalli were unsuccessful
Researchers attempted to grow and isolate basidiomycete cells independent from their lichen partners, the algae and the ascomycete fungus. Often times it is very difficult to culture new organisms because we do not know enough about the growth requirements. This is frequently the case with organisms that form symbiotic relationships, as they often lose the ability to grow independent of their symbiotic partners.
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we designed specific primers for ribosomal DNA [rDNA; 18S, internal transcribed spacer (ITS), and D1D2 domains of 28S) to screen lichens growing physically adjacent to Bryoria in Montana forests.
Primers are small oligonucleotide sequences that are used as probes to determine if something is present in an unknown mixed sample. In this case, the primer is designed to match a piece of ribosomal DNA specifically in basidiomycete genomes found in the previous experiments. If the primer finds a target in a biological sample it is highly likely that a basidiomycete is present in the sample. In these experiments, the biological samples are other wild lichens found next to Bryoria lichens in Montana forests. Primers operate on the molecular level, and so very little biological material is needed to determine if basidiomycetes are present.
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expanding the taxonomic range to consider all Fungi, we found 506 contigs with significantly higher abundances in vulpinic acid–rich B. tortuosa thalli
The author initially looked only at the expressed gene copies (contiguous sections of messenger RNA, or contigs) that corresponded either to known ascomycete or known algal DNA. They limited their search to these two because until then, a lichen was thought to only consist of those two partners. When they could not find any difference that would explain the phenotype differences between the two lichens, they expanded their search to see what other kinds of DNA was found in every single lichen, and perhaps had not been accounted for yet. They found 506 contiguous snippets of DNA that were found in every lichen that appeared to come from a second fungus, a basidiomycete, that wasn’t supposed to occur in lichens.
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transcriptome-wide analysis
A transcriptome is a way for researchers to count the number of messenger RNA copies that has been produced from each gene in an organism, which is a measure of how much this gene is expressed. By comparing the level of gene expression between two different species, researchers can get an idea of which genes might be involved in producing different phenotypes in those species.
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These two species have been distinguished for 90 years by the thallus-wide production of the toxic substance vulpinic acid in B. tortuosa, causing it to appear yellowish, in contrast to B. fremontii, which is dark brown (11). Recent phylogenetic analyses have failed to detect any fixed sequence differences between the two species
While these two lichens look very similar, there is an important distinction. There is evidence that Bryoria fremontii has been used and consumed by Indigenous populations for centuries, while Bryoria tortuosa contains a yellowish substance, vulpinic acid, that is toxic to mammals. Indigenous peoples soaked Bryoria collected for food, and it is thought this may have helped rinse background levels of vulpinic acid from mixed samples. Despite this difference between the two lichen species, scientists had been unable to determine a phylogenetic distinction.
Read more in Scientific American: https://blogs.scientificamerican.com/artful-amoeba/2-lichen-mysteries-solved-reveal-a-greater-hidden-truth/
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molecular clock
The molecular clock theory posits that changes (mutations) occur at a constant rate, and that we can use the number of changes between any two sequences to find out approximately when the sequences diverged from one another. To apply a molecular clock to a phylogeny one must use a rooted tree (see Figure 2A).
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phylogenomic
Data used to reconstruct evolutionary relationships, such as in a phylogenetic tree, except extracted at the scale of the whole genome.
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contigs
From the word contiguous, meaning a continuous set of DNA sequences.
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photobiont
The photosynthesizing partner in the symbiotic relationship; in this case, a type of alga.
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lichen symbiosis
Watch a video from the Havard Museum of Natural History about what defines a lichen. This video describes lichens, symbiosis, and the lichen life cycle. Notice that the video makes no reference to basidiomycete yeasts.
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over 140 years
Well-known children's book author Beatrix Potter was one of the earliest proponents of the symbiotic nature of lichens in the English-speaking world.
Read more in the BBC: http://www.bbc.com/earth/story/20160215-beatrix-potter-pioneering-scientist-or-passionate-amateur
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cohort
Group.
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cis-vaccenyl acetate (cVA)
Since flies do not have verbal language, they communicate with one another by releasing and responding to chemicals known as chemosensory cues. Different cues can have different meanings. For instance, some cues released by the female can signal to the male that she is ready to mate. Other cues, like the one described here (cVA), can signal that the female is no longer looking to mate, thus driving away any unwanted males.
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system regulates acute ethanol sensitivity in Drosophila
Past research has shown that interactions between neuropeptide F and its corresponding receptor can alter how much flies are affected by alcohol consumption.
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NPY receptor homolog NPR-1 regulates ethanol behaviors
Past research has shown that individual differences in alcohol tolerance amongst C. elegans are related to natural variations in the amount of neuropeptide Y receptor found in their brains.
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When tested 24 hours later, males in the experimental group demonstrated strong preference for the odor associated with NPF neuron activation. The genetic controls, which did not undergo NPF neuron activation, but were exposed to the same training protocol, developed no odor preference (Fig. 4C). Other controls, which underwent NPF neuron activation but were not exposed to the training protocol, similarly developed no odor preference (fig. S6C).
The researchers found that the flies who had learned to associate an odor with activation of the NPF circuit preferred that odor in the Y maze, relative to the unpaired/neutral odor.
Other control flies who underwent partial genetic manipulations but did not experience NPF activity-odor pairings had no odor preference in the maze.
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surfeit
Excess.
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deficit
Shortage.
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Rejected-isolated males showed the lowest transcript levels, virgin-grouped males showed higher levels, and mated-grouped males showed the highest (Fig. 2A and fig. S4). Rejected-isolated males also showed markedly lower NPF protein levels than mated-grouped males
The researchers found that flies that had experienced sexual rejection had significantly reduced levels of NPF in their brain, and flies that had undergone mating had significantly increased levels of NPF. This supports the hypothesis that sexual history can affect the amount of NPF that gets made in the brain, which can in turn change how much alcohol an organism might consume.
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Intriguingly, stressful experiences regulate mammalian NPY levels.
Past research has also shown that the amount of neuropeptide Y found in a rodent's brain is related to the amount of stress they might experience during their life.
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neuropeptide Y [NPY
A mammalian version of neuropeptide F. This molecule is found in the human brain.
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the complexity of the evolutionary history of dogs
For a recent study on the history of dogs in the Americas (published by some of the same authors of this paper), check out the 2018 research article in the "Related content" tab.
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although this dog was likely able to digest starch less efficiently than modern dogs, it was able to do so more efficiently than wolves
The ability to digest starch was important to look at, because it gives an idea of when dogs were domesticated, and who domesticated them—hunter-gatherers (meat-based diet) or farmers (starch-based diet).
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